Hannah was a target of a kidnap plot orchestrated by The G-Man, who wanted to use her against her father John Robertson who was newly appointed administrator of City 17 after Wallace Breen's death. Nathan Johnson kidnapped Hannah and took her to a hideout owned by the G-Man. G-Man forced John to step down as administrator and instead appoint G-Man. G-Man then took Hannah to the citadel, but planned to have her executed instead of released. Nathan felt guilty and turned on G-Man, who tried to flee in a teleporter. Nathan faced off with him and destroyed the portal, presumably killing G-Man.
The events of the abduction were prevented when Nathan and G-Man ended up changing time when they traveled to the past. In this slightly modified timeline, Hannah was on friendly terms with Nathan, although Frank still held a grudge towards her.
Hannah later left City 17 with her father, who got a new job in City 15.
Return to City 17
Hannah returned two-years later after she had an argument with her father so went to stay with Nathan. Nathan returned Hannah to John.
When G-Man resurfaced under the identity of Frank Blackstone he plotted revenge on both Hannah and Nathan for "ruining" him in the past. While Hannah was home alone, Frank accessed the house and attempted to kidnap her again, but this time failed as Hannah fought him off and escaped.
Nathan got informed that Hannah had been murdered in her bed, the cause of death being strangulation. Nathan was visited by a "ghost" belonging to Hannah, who informed him that Frank was responsible. Nathan avenged her demise by "killing" Frank in the Xen dimension by firing a portal at him.
Hannah existed in a brand new continuity which Nathan ended up in, which was a universe created from a merge between the Half-Life universe and real life. In this world, she was a composite of the primary universe Hannah Robertson, Samantha Johnson and Emile Clayton.
In this timeline she is the daughter of Jackie Robertson, who is the administrator of the New City 17 following the death of Wallace Breen. Jackie hires Nathan as Hannah's bodyguard, although Nathan finds the girl annoying due to her constant talking. Hannah ends up kidnapped by a Spy posing as Nathan and brought to Wallace Breen's older brother "the Administrator", as he feels he has the right to control of City 17. Nathan is accused of the abduction, but proves his innocence when he exposes the Spy and rescues Hannah from the Administrator, who ends up being imprisoned at Nova Prospekt by Jackie.